Replication Timing Quantification
Replication Timing Quantification - Related Videos
17:14
Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization
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Cited by 11 •
2012
A quantitative method for the analysis of chromosome replication timing is described. The method utilizes BrdU incorporation in combination with fluorescent in situ hybridization (FISH) to assess replication timing of mammalian chromosomes. This technique allows for the direct comparison of rearranged and un-rearranged chromosomes within the same cell.
08:06
Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
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Cited by 6 •
2017
We describe here a relatively fast and simple approach for mapping genome-wide mammalian replication timing, from cell isolation to the basic analysis of the sequencing results. A genomic map of a representative replication program will be provided following the protocol.
02:31
Chromosome Replication
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2020
Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins. This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin of...
10:17
Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System
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Cited by 5 •
2018
Zebrafish were recently used as an in vivo model system to study DNA replication timing during development. Here is detailed the protocols for using zebrafish embryos to profile replication timing. This protocol can be easily adapted to study replication timing in mutants, individual cell types, disease models, and other species.
02:40
DNA Replication
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2020
DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied. After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells. Replication in Prokaryotes DNA replication uses a large number of...
FAQs
During S phase, DNA collected from cells at different replication stages contains different amounts of sequences from regions that have already duplicated. Comparing those abundances across stages reveals when each genomic region becomes enriched, allowing profiles to classify replication as earlier or later. The resulting timing pattern can then be examined alongside chromatin organization, gene activity, or genome stability.
Synchronization places sampled cells at defined stages of S phase, so sequence abundance can be compared between corresponding stages rather than across a mixed population. This makes it easier to identify regions enriched early or late in the replication program. The resulting profiles can be compared among biological states, including differentiated cells or conditions associated with replication stress.
Timing profiles provide a genome-wide pattern that can be related to chromatin organization and gene activity, rather than serving only as a record of DNA synthesis. They also support examination of genome stability and changes during development. These relationships help researchers interpret replication timing as one feature of broader genome regulation.
Both approaches can identify genomic regions that become enriched in DNA collected from different replication stages. DNA sequencing provides sequence-based measurements, while hybridization offers another way to assess stage-specific enrichment. In either case, comparing signals across stages produces a replication-timing profile that can be related to cellular state and genome regulation.
A workflow begins with cells sampled at different stages of S phase, often using synchronized populations. DNA is collected from those samples, and sequence abundance is measured by DNA sequencing or hybridization. Researchers compare the measurements across stages to identify regions enriched early or late, then represent the results as a genome-wide replication-timing profile.
It is useful when researchers need to characterize genome regulation across biological states. Profiles can be compared during differentiation or development, and they can reveal alterations associated with disease or replication stress. Relating these changes to chromatin organization, gene activity, and genome stability helps place altered DNA synthesis within a broader biological context.